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Lu YN, Lan JP, Mao YJ, Wang YX, Mei GJ, Shi F. Catalytic asymmetric de novo construction of dihydroquinazolinone scaffolds via enantioselective decarboxylative [4+2] cycloadditions. Chem Commun (Camb) 2018; 54:13527-13530. [DOI: 10.1039/c8cc08282k] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The first de novo construction of enantioenriched dihydroquinazolinones via an intermolecular strategy has been established. This approach also represents the first catalytic asymmetric [4+2] cycloaddition of vinyl benzoxazinanones with sulfonyl isocyanates.
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Affiliation(s)
- Yi-Nan Lu
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
| | - Jin-Ping Lan
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
| | - Yu-Jia Mao
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
| | - Ye-Xin Wang
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
| | - Guang-Jian Mei
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
| | - Feng Shi
- School of Chemistry and Materials Science
- Jiangsu Normal University
- Xuzhou
- China
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2
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Samanta PN, Das KK. Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Dutta S, Kotha SS, Sekar G. Metal free one-pot synthesis of α-ketoamides from terminal alkenes. RSC Adv 2015. [DOI: 10.1039/c5ra05671c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A practical approach towards the synthesis of α-ketoamides from terminal alkenes has been developed using I2/IBX under one-pot reaction conditions.
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Affiliation(s)
- Sayan Dutta
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai
- India
| | | | - Govindasamy Sekar
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai
- India
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4
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Sanz-Marco A, García-Ortiz A, Blay G, Pedro JR. Catalytic asymmetric conjugate addition of terminal alkynes to β-trifluoromethyl α,β-enones. Chem Commun (Camb) 2014; 50:2275-8. [DOI: 10.1039/c3cc48508k] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The first enantioselective conjugate alkynylation of β-trifluoromethyl α,β-enones using terminal alkynes and a taniaphos–Cu(i) complex as catalyst is described.
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Affiliation(s)
- Amparo Sanz-Marco
- Departament de Química Orgànica
- Facultat de Química
- Universitat de València
- 46100-Burjassot, Spain
| | - Andrea García-Ortiz
- Departament de Química Orgànica
- Facultat de Química
- Universitat de València
- 46100-Burjassot, Spain
| | - Gonzalo Blay
- Departament de Química Orgànica
- Facultat de Química
- Universitat de València
- 46100-Burjassot, Spain
| | - José R. Pedro
- Departament de Química Orgànica
- Facultat de Química
- Universitat de València
- 46100-Burjassot, Spain
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5
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Linder M, Ranganathan A, Brinck T. “Adapted Linear Interaction Energy”: A Structure-Based LIE Parametrization for Fast Prediction of Protein–Ligand Affinities. J Chem Theory Comput 2012; 9:1230-9. [DOI: 10.1021/ct300783e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mats Linder
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
| | - Anirudh Ranganathan
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
| | - Tore Brinck
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
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6
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Reynolds C, de Koning CB, Pelly SC, van Otterlo WAL, Bode ML. In search of a treatment for HIV--current therapies and the role of non-nucleoside reverse transcriptase inhibitors (NNRTIs). Chem Soc Rev 2012; 41:4657-70. [PMID: 22618809 DOI: 10.1039/c2cs35058k] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human immunodeficiency virus (HIV) causes AIDS (acquired immune deficiency syndrome), a disease in which the immune system progressively deteriorates, making sufferers vulnerable to all manner of opportunistic infections. Currently, world-wide there are estimated to be 34 million people living with HIV, with the vast majority of these living in sub-Saharan Africa. Therefore, an important research focus is development of new drugs that can be used in the treatment of HIV/AIDS. This review gives an overview of the disease and addresses the drugs currently used for treatment, with specific emphasis on new developments within the class of allosteric non-nucleoside reverse transcriptase inhibitors (NNRTIs).
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Affiliation(s)
- Chevonne Reynolds
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, South Africa
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7
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Minkara MS, Davis PH, Radhakrishnan ML. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT. Proteins 2011; 80:573-90. [DOI: 10.1002/prot.23221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 10/06/2011] [Indexed: 11/09/2022]
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8
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Zhang H, Qin F, Ye W, Li Z, Ma S, Xia Y, Jiang Y, Zhu J, Li Y, Zhang J, Chen HF. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des 2011; 78:427-37. [DOI: 10.1111/j.1747-0285.2011.01163.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Boonsri P, Kuno M, Hannongbua S. Key interactions of the mutant HIV-1 reverse transcriptase/efavirenz: an evidence obtained from ONIOM method. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00162k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Li Z, Zhang H, Li Y, Zhang J, Chen HF. Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. Chem Biol Drug Des 2010; 77:63-74. [PMID: 21134218 DOI: 10.1111/j.1747-0285.2010.01049.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diaryltriazine inhibitors have highly potent and effective bioactivities for the wild type of HIV-1 reverse transcription. To design new drug of antimutant HIV-1 reverse transcriptase, the mechanism of drug resistance for four types of mutants was revealed. Molecular dynamics simulations suggest that Lys101, Leu100, Lys103, Tyr181, and Tyr188 are key residues. Different mutants of key residues may have different interaction modes and lead to different drug resistances. Then, CoMFA and CoMSIA methods were employed to construct 3D quantitative structure-activity relationship models. These models were evaluated by test set compounds. These models can be used to make quantitative prediction of their bioactivities for lead compounds before resorting to in vitro and in vivo experimentation.
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Affiliation(s)
- Zeng Li
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
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11
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La Regina G, Coluccia A, Silvestri R. Looking for an active conformation of the future HIV type-1 non-nucleoside reverse transcriptase inhibitors. Antivir Chem Chemother 2010; 20:213-37. [PMID: 20710063 DOI: 10.3851/imp1607] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
HIV type-1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key drugs of highly active antiretroviral therapy (HAART) in the clinical management of AIDS/HIV infection. NNRTI-based HAART regimes effectively suppress viral reproduction, are not cytotoxic and show favourable pharmacokinetic properties. First-generation NNRTIs suffer the rapid selection of viral variants, hampering the binding of inhibitors into the reverse transcriptase (RT) non-nucleoside binding site (NNBS). Efforts to improve these first inhibitors led to the discovery of second-generation NNRTIs that proved to be effective against the drug-resistant mutant HIV-1 strains. The success of such agents launched a new season of NNRTI design and synthesis. This paper reviews the characteristics of second-generation NNRTIs, including etravirine, rilpivirine, RDEA-806, UK-453061, BIRL 355 BS, IDX 899, MK-4965 and HBY 097. In particular, the binding modes of these inhibitors into the NNBS of the HIV-1 RT and the most clinically relevant mutant RTs are analysed and discussed.
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Affiliation(s)
- Giuseppe La Regina
- Department of Chimica e Tecnologie del Farmaco, Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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12
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Prajapati DG, Ramajayam R, Yadav MR, Giridhar R. The search for potent, small molecule NNRTIs: A review. Bioorg Med Chem 2009; 17:5744-62. [PMID: 19632850 DOI: 10.1016/j.bmc.2009.06.060] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/22/2009] [Accepted: 06/23/2009] [Indexed: 11/29/2022]
Abstract
AIDS has become the leading pandemic disease, and is the cause of death worldwide. Presently, HAART treatment, a combination of reverse transcriptase (RT) and protease inhibitors is also unsuccessful due to the virus getting resistant to the drugs because of mutational changes. Two types of RT inhibitors exist namely nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The NNRTIs which bind to an allosteric site on RT are an important arsenal of drugs against HIV-1. The specificity of NNRTIs towards HIV-1 has led to extensive structural and molecular modelling studies of enzyme complexes and chemical synthesis of second and third-generation NNRTIs. The major drawbacks of NNRTIs are generation of resistance and pharmacokinetic problems. By mutational studies of non-nucleoside inhibitor binding pocket (NNIBP) some amino acids which were found to play an important role in proper binding resulted less prone to mutation. In this review we present a chronological history of NNRTI development, also highlighting the need for small molecules belonging to the NNRTI class for the management of AIDS.
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Affiliation(s)
- Dhaval G Prajapati
- Pharmacy Department, Kalabhavan, The M.S. University of Baroda, Vadodara, India
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13
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Srivab P, Hannongbua S. A Study of the Binding Energies of Efavirenz to Wild-Type and K103N/Y181C HIV-1 Reverse Transcriptase Based on the ONIOM Method. ChemMedChem 2008; 3:803-11. [DOI: 10.1002/cmdc.200700181] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Smith MBK, Rader LH, Franklin AM, Taylor EV, Smith KD, Smith RH, Tirado-Rives J, Jorgensen WL. Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz. Bioorg Med Chem Lett 2007; 18:969-72. [PMID: 18166457 DOI: 10.1016/j.bmcl.2007.12.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 12/12/2007] [Accepted: 12/14/2007] [Indexed: 10/22/2022]
Abstract
The effect of mutations on amino acid residues L100, V106, and Y181 for unbound HIV-1 reverse transcriptase (RT) and RT bound to nevirapine and efavirenz was investigated using Monte Carlo/free energy perturbation calculations. Using both native and bound crystal structures of RT, mutation of the amino acid residues to both those observed and unobserved in patients was carried out. The results of the calculations revealed that the variant that survives in patients dosed with either nevirapine or efavirenz had a more positive Delta Delta G value than other variants that were not observed in patients. These data suggest that the mutation observed in patients is the most effective (the one that binds the drug most weakly) of all possible codon change mutations.
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15
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Yoshida T, Yamagishi K, Chuman H. QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio
MO Calculation of Their Complex Structures with HIV-1 PR. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200730108] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E. Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097. J Mol Biol 2006; 365:77-89. [PMID: 17056061 DOI: 10.1016/j.jmb.2006.08.097] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 08/22/2006] [Indexed: 11/16/2022]
Abstract
Lys103Asn and Tyr181Cys are the two mutations frequently observed in patients exposed to various non-nucleoside reverse transcriptase inhibitor drugs (NNRTIs). Human immunodeficiency virus (HIV) strains containing both reverse transcriptase (RT) mutations are resistant to all of the approved NNRTI drugs. We have determined crystal structures of Lys103Asn/Tyr181Cys mutant HIV-1 RT with and without a bound non-nucleoside inhibitor (HBY 097, (S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthio-methyl)-3,4-dihydroquinoxalin-2(1H)-thione) at 3.0 A and 2.5 A resolution, respectively. The structure of the double mutant RT/HBY 097 complex shows a rearrangement of the isopropoxycarbonyl group of HBY 097 compared to its binding with wild-type RT. HBY 097 makes a hydrogen bond with the thiol group of Cys181 that helps the drug retain potency against the Tyr181Cys mutation. The structure of the unliganded double mutant HIV-1 RT showed that Lys103Asn mutation facilitates coordination of a sodium ion with Lys101 O, Asn103 N and O(delta1), Tyr188 O(eta), and two water molecules. The formation of the binding pocket requires the removal of the sodium ion. Although the RT alone and the RT/HBY 097 complex were crystallized in the presence of ATP, only the RT has an ATP coordinated with two Mn(2+) at the polymerase active site. The metal coordination mimics a reaction intermediate state in which complete octahedral coordination was observed for both metal ions. Asp186 coordinates at an axial position whereas the carboxylates of Asp110 and Asp185 are in the planes of coordination of both metal ions. The structures provide evidence that NNRTIs restrict the flexibility of the YMDD loop and prevent the catalytic aspartate residues from adopting their metal-binding conformations.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854, USA
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17
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Pungpo P, Saparpakorn P, Wolschann P, Hannongbua S. Computer-aided molecular design of highly potent HIV-1 RT inhibitors: 3D QSAR and molecular docking studies of efavirenz derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2006; 17:353-70. [PMID: 16920659 DOI: 10.1080/10629360600884520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ligand- and structure-based design approaches have been applied to an extended series of 74 efavirenz compounds effectively inhibiting wild type (WT) and mutant type (K103N) HIV-1 reverse transcriptase (RT). For ligand-based approach, three dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA), were performed. The starting geometry of efavirenz was obtained from X-ray crystallographic data. The efavirenz derivatives were constructed and fully optimized by ab-initio molecular orbital method at HF/3-21G level. Reliable QSAR models for high predictive abilities were developed. Regarding WT and K103N inhibitions, CoMFA models with r2/cv = 0.651 and 0.678 and CoMSIA models with r2/cv = 0.662 and 0.743 were derived, respectively. The interpretation obtained from the models highlights different structural requirements for inhibition of WT and K103N HIV-1 RT. To elucidate potential binding modes of efavirenz derivatives in the binding pocket of WT and K103N HIV-1 RT, structure-based approach based on computational docking studies of selected efavirenz compounds were performed by using GOLD and FlexX programs. The results derived from docking analysis give additional information and further probe the inhibitor-enzyme interactions. The correlation of the results obtained from 3D QSAR and docking models validate each other and lead to better understanding of the structural requirements for the activity. Therefore, these integrated results are informative to provide key features and a helpful guideline for novel compound design active against HIV-1 RT.
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Affiliation(s)
- P Pungpo
- Faculty of Science, Ubonratchathani University, Warinchamrap, UbonRatchathani, 34190, Thailand.
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18
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Himmel DM, Das K, Clark AD, Hughes SH, Benjahad A, Oumouch S, Guillemont J, Coupa S, Poncelet A, Csoka I, Meyer C, Andries K, Nguyen CH, Grierson DS, Arnold E. Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: a new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains. J Med Chem 2006; 48:7582-91. [PMID: 16302798 DOI: 10.1021/jm0500323] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the treatment of AIDS, the efficacy of all drugs, including non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), has been limited by the rapid appearance of drug-resistant viruses. Lys103Asn, Tyr181Cys, and Tyr188Leu are some of the most common RT mutations that cause resistance to NNRTIs in the clinic. We report X-ray crystal structures for RT complexed with three different pyridinone derivatives, R157208, R165481, and R221239, at 2.95, 2.9, and 2.43 A resolution, respectively. All three ligands exhibit nanomolar or subnanomolar inhibitory activity against wild-type RT, but varying activities against drug-resistant mutants. R165481 and R221239 differ from most NNRTIs in that binding does not involve significant contacts with Tyr181. These compounds strongly inhibit wild-type HIV-1 RT and drug-resistant variants, including Tyr181Cys and Lys103Asn RT. These properties result in part from an iodine atom on the pyridinone ring of both inhibitors that interacts with the main-chain carbonyl oxygen of Tyr188. An acrylonitrile substituent on R165481 substantially improves the activity of the compound against wild-type RT (and several mutants) and provides a way to generate novel inhibitors that could interact with conserved elements of HIV-1 RT at the polymerase catalytic site. In R221239, there is a flexible linker to a furan ring that permits interactions with Val106, Phe227, and Pro236. These contacts appear to enhance the inhibitory activity of R221239 against the HIV-1 strains that carry the Val106Ala, Tyr188Leu, and Phe227Cys mutations.
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Affiliation(s)
- Daniel M Himmel
- Center for Advanced Biotechnology and Medicine (CABM) and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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Das K, Lewi PJ, Hughes SH, Arnold E. Crystallography and the design of anti-AIDS drugs: conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2005; 88:209-31. [PMID: 15572156 DOI: 10.1016/j.pbiomolbio.2004.07.001] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Drug resistance is a key cause of failure for treatment of HIV infection. The efficacy of non-nucleoside reverse transcriptase inhibiting (NNRTI) drugs is impaired by rapid emergence of drug-resistance mutations. A multidisciplinary effort led to the discovery of the potent NNRTIs dapivirine and etravirine, both of which are diarylpyrimidine (DAPY) derivatives. Systematic structural and molecular modeling studies of HIV-1 reverse transcriptase (RT)/NNRTI complexes revealed different modes of inhibitor binding, and some of the DAPY inhibitors can bind to RT in different conformations. The torsional flexibility ("wiggling") of the inhibitors can generate numerous conformational variants and the compactness of the inhibitors permits significant repositioning and reorientation (translation and rotation) within the pocket ("jiggling"). Such adaptations appear to be critical for the ability of the diarylpyrimidine NNRTIs to retain their potency against a wide range of drug-resistant HIV-1 RTs. Exploitation of inhibitor conformational flexibility (such as torsional flexibility about strategically located chemical bonds) can be a powerful element of drug design, especially for the design of drugs that will be effective against rapidly mutating targets (which is a collection of related targets).
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Affiliation(s)
- Kalyan Das
- Department of Chemistry and Chemical Biology, Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane West, Piscataway, NJ 08854, USA
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Rodríguez-Barrios F, Gago F. Understanding the basis of resistance in the irksome Lys103Asn HIV-1 reverse transcriptase mutant through targeted molecular dynamics simulations. J Am Chem Soc 2005; 126:15386-7. [PMID: 15563158 DOI: 10.1021/ja045409t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Results of targeted molecular dynamics simulations confirm the existence of a higher energy barrier for creation of the pocket where non-nucleoside reverse transcriptase inhibitors bind in the K103N mutant enzyme relative to wild-type.
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Das K, Clark AD, Lewi PJ, Heeres J, De Jonge MR, Koymans LMH, Vinkers HM, Daeyaert F, Ludovici DW, Kukla MJ, De Corte B, Kavash RW, Ho CY, Ye H, Lichtenstein MA, Andries K, Pauwels R, De Béthune MP, Boyer PL, Clark P, Hughes SH, Janssen PAJ, Arnold E. Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. J Med Chem 2004; 47:2550-60. [PMID: 15115397 DOI: 10.1021/jm030558s] [Citation(s) in RCA: 389] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anti-AIDS drug candidate and non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC125-R165335 (etravirine) caused an initial drop in viral load similar to that observed with a five-drug combination in naïve patients and retains potency in patients infected with NNRTI-resistant HIV-1 variants. TMC125-R165335 and related anti-AIDS drug candidates can bind the enzyme RT in multiple conformations and thereby escape the effects of drug-resistance mutations. Structural studies showed that this inhibitor and other diarylpyrimidine (DAPY) analogues can adapt to changes in the NNRTI-binding pocket in several ways: (1). DAPY analogues can bind in at least two conformationally distinct modes; (2). within a given binding mode, torsional flexibility ("wiggling") of DAPY analogues permits access to numerous conformational variants; and (3). the compact design of the DAPY analogues permits significant repositioning and reorientation (translation and rotation) within the pocket ("jiggling"). Such adaptations appear to be critical for potency against wild-type and a wide range of drug-resistant mutant HIV-1 RTs. Exploitation of favorable components of inhibitor conformational flexibility (such as torsional flexibility about strategically located chemical bonds) can be a powerful drug design concept, especially for designing drugs that will be effective against rapidly mutating targets.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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Udier-Blagović M, Tirado-Rives J, Jorgensen WL. Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues. J Med Chem 2004; 47:2389-92. [PMID: 15084137 DOI: 10.1021/jm0303507] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of the K103N mutation of HIV-1 reverse transcriptase (RT) on the activity of efavirenz analogues was studied via Monte Carlo/free energy perturbation calculations. The relative fold resistance energies indicate that efavirenz binds to K103N RT in a manner similar to the wild-type enzyme. The improved performance of the quinazolinones against the mutant enzyme is attributed to formation of a more optimal hydrogen-bonding network with bridging water molecules between the ligands and Glu138.
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Abstract
An overview is given on the diverse uses of computational chemistry in drug discovery. Particular emphasis is placed on virtual screening, de novo design, evaluation of drug-likeness, and advanced methods for determining protein-ligand binding.
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24
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Ostrovsky D, Udier-Blagović M, Jorgensen WL. Analyses of Activity for Factor Xa Inhibitors Based on Monte Carlo Simulations. J Med Chem 2003; 46:5691-9. [PMID: 14667222 DOI: 10.1021/jm030288d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monte Carlo/Extended Linear Response (MC/ELR) simulations have been conducted on 60 inhibitors of human factor Xa to determine the important interactions associated with their activity. A variety of physicochemical descriptors were configurationally averaged during the course of the simulations of each inhibitor bound to factor Xa and free in water. A regression equation was then derived; it reproduces the experimental inhibition data with a correlation coefficient, r(2), of 0.74, an rms error of 0.67 kcal/mol, and an average unsigned error of 0.60 kcal/mol using only two physically reasonable descriptors. The two factors that emerged as important in determining inhibitory potential are (1) favorable van der Waals interactions between protein and ligand and (2) direct hydrogen bonding between the inhibitor and protein. The conclusions were supported with structural analyses and results of MC/free energy perturbation (FEP) calculations.
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Affiliation(s)
- Dennis Ostrovsky
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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